Reporter, a term coined by the MAGE object model refers to
spotted DNA sequence on a microarray. Reporters are
therefore usually described by a sequence and a series of
database identifiers qualifying that sequence. Reporters are
generally understood as the thing biologists are interested
in when carrying out DNA microarray experiments.

In BASE, reporters also refer to Affymetrix Probeset ID but
reporters can be used to describe genes, transcripts, exons
or any other sequence entity of biological relevance.

9.1. Reporter types

Reporter Type
allows classification of reporters based on their usage
and qualification defined during the array design
specification.
You can manage the reporter types by going to
AdministrateTypesReporter types.

Figure 9.1. Reporter type properties

Name

The name of the reporter type. It is advised to define the name
so that it is compatible with the
MIAME requirements
and recommendations issues by microarray data
repositories. Alternately, the local reporter type
could be submitted to those repositories for term
inclusion.

Description

A description of the reporter type.

9.2. Reporters

Go to
ViewReporters to view and manage the reporters.

9.2.1. Import/update reporter from files

Reporters are used to represent genes, transcripts,
exons and therefore come in their thousands. To solve
this problem, BASE relies on
Reporter import plug-ins.
Those need to be specifically configured to deal with
a particular input file format. This input file can be
typically be an Axon GAL file or an Affymetrix CSV file
which both provide information about reporters and their
annotations. See Chapter 19, Import of data
for more information about importing and Section 22.2, “Plug-in configurations”
for more information about configuring file formats.

Dealing with Affymetrix probesets

In BASE, Affymetrix probesets should be treated as reporters.
The probeset ID could be stored in both the
Name and the External ID
fields of the reporter table.
Storing the probeset ID should be enough
as most analysis tools allow retrieval of updated
information based on the probeset ID from
web resources.

For some Affymetrix chips the associated CSV file does not
list all reporters on the actual chip. This will lead to
problems in later use of the affected chip types. Simply use
the associated CDF file to import the missing probesets into
BASE, make sure not to upgrade existing reporters when
starting the plug-in.

9.2.2. Manual management of reporters

Reporters can also be created or edited manually
one-by-one. This follows the same pattern as for
all other items and is described in general terms
in Section 5.3, “Working with items”.

Figure 9.2. Reporter properties

This tab shows core information that would be
common to all BASE instances.

Name

The name of the reporter. This is often the same
as the External ID.

External ID

The external ID of the reporter as it is defined in
some database. The ID must be unique within BASE. The
external ID is what plug-ins uses to match reporter
information found in raw data files, array design files,
etc.

Type

Optionally select a reporter type.

Gene symbol

The gene this reporter represents.

Figure 9.3. Extended reporter properties

Reporters belong to a special class whose properties
can be defined and extended by system
administrators. This is done by modifying the
extended-properties.xml file during
database configuration or upgrade. All fields on
this tab are automatically generated based on this
configuration and can be different from one server
to the next.
See Section 21.2, “Installation instructions”
and Appendix C, extended-properties.xml reference
for more information.

Note

It is possible to configure the extended properties
so that links to the primary external databases can
be made. For example, the Cluster ID
is linked to the UniGene database at NCBI.

9.2.3. Deleting reporters

Deleted reporters cannot be restored

Reporters are treated differently from other
items (e.g biosources or protocols) since they
does not use the trashcan mechanism (see
Section 5.5, “Trashcan”).
The deletion happens immediately and is an unrecoverable
event. BASE will always show a warning message which you must
confirm before the reporters are deleted.

Reporters which has been referenced to from reporter lists, raw data, array
designs, plates or any other item cannot be deleted.

Batch deletion

A common problem is to delete reporters that has been accidentally
created. The regular web interface is usually no good since it
only allows you to delete a limited number of reporters at a time. To solve
this problem the reporter import plug-in can be used in delete mode.
You can use the same file as you used when importing. Just select
the delete option for the mode
parameter in the configuration wizard and continue as usual.
If the plug-in is used in delete mode from a reporter list it will
only remove the reporters from the reporter list. The reporters are not
deleted from the database.

Note

It may be a bit confusing to delete things from an import plug-in. But
since plug-ins can only belong to one category and we wanted to re-use
existing file format definitions this was our only option.

9.3. Reporter lists

BASE allows for defining sets of reporters for a
particular use, for instance to define a list of
reporters to be used on an array. There are several ways to do
so:

Use the New reporter list button on the
ViewReporters page. This creates a reporter list with the current
selection or filtered out reporters.

Use the New button on the
ViewReporter lists page. This creates an initially empty reporter list
that can be filled later.

Use the New reporter list button on the
Features tab on the single-item view page
for an array design. This creates a reporter list with all or some of
the reporters used on the array design.

Use the New reporter list button on the
Raw data tab on the single-item view page
for a raw bioassay. This creates a reporter list with all or some of
the reporters used by the raw bioassay.

Use the New reporter list button on the
Spot data tab on the single-item view page
for a bioassay set in the experiment analysis section.
This creates a reporter list with all or some of
the reporters used by the current bioassay set.

Use the New reporter list button on the
Reporter search tab in experiment explorer.
This creates a reporter list with all or some of
the reporters used by the current bioassay set.

Figure 9.4.
The Create reporter list called from
the reporters page.

Name

The name of the reporter list.

External ID

An optional external ID. This value is useful,
for example, for a tool that automatically
updates the reporter list from some external source.
It is not used by BASE.

Which reporters

Select one of the options for specifying which reporters
should be included in the list. This option is only available
when creating a new reporter list, not when editing an existing
list. The default is to create a list with all
reporters that are in the current list.

Description

A description of the reporter list.

Tip

To add or remove reporters to the list use the
Reporters tab on the single-item
view page of a reporter list. This tab lists all
reporters in the list and there are functions for
removing, adding and importing reporters to the list.

9.3.1. Merging reporter lists

It is possible to modify a reporter list by merging it with other reporter
lists. Go to the single-item view page for a reporter list. There should be
three buttons in the toolbar corresponding to three main merge variants:

Union: Add all reporters from
the source lists to the destination list.

Intersection: Keep only reporters
that are present in all selected lists.

Complement: Keep only reporters that
are unique for the destination list.

All three buttons open up the same dialog with different default selections.

Figure 9.5. Merge reporter lists

This list

Shows the name of the current reporter list.

What to do

In this drop-down list you can select if you want to
add, keep
or remove reporters from the
selected list based on if a reporter is present in one
or all of some other reporter lists (selected below).
The image to the right gives an overview what will
happen for the currently selected alternatives. The
red-colored areas indicate which reporters that are
included in the final list. The white-colored areas
indicate reporters that doesn't pass the filter and
are excluded from the final list.